


The Whole Equation

by esteefee



Category: Stargate Atlantis
Genre: Alternate Universe - Canon, Alternate Universe - Stargate Atlantis, Artificial Intelligence, Cybernetics, Hive Mind, M/M, Prosthesis, Sentient Atlantis, War
Language: English
Status: Completed
Published: 2014-09-08
Updated: 2014-09-08
Packaged: 2018-02-16 14:16:28
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 17,953
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2272887
Author URL: https://archiveofourown.org/users/esteefee/pseuds/esteefee
Summary: <blockquote class="userstuff">
              <p>Two years after being reassigned for medical reasons, Commander John Sheppard is recalled by Atlantis to be its Pilot-Captain once again. He's thrown into a political situation he really doesn't understand, Atlantis is keeping secrets from him, and—oh, yeah—his ex, Rodney McKay, really wishes he'd kiss off.</p>
            </blockquote>





	The Whole Equation

**Author's Note:**

> Please read the ending notes for warnings if you have any triggers (the tags should provide some clue). The warnings do contain spoilers.
> 
> This story is loosely based on one of the alternate universes from _The Daedalus Variations_.
> 
> Today marks my 10 year anniversary as a fiction writer! Many thanks to Mischief5 for the research help, the brainstorming, the beta editing, and listening to my kvetching. This story would not have been possible without her, and certainly not within one mad week.

[](http://ic.pics.livejournal.com/esteefee/14783436/137321/137321_original.png)

John slid down the ladder and dropped to the hanger deck, giving a casual salute to the ground crew as they started to scramble all over his F-306 for the post-flight check. He didn't indulge often anymore, but when he took one of his babies up, the crew was always extra diligent afterward, as if their training commander hadn't forgotten more about these ships than they could remember on a good day.

Well, let them fret. The skies had been a rare, clear blue above M8B-753, or Tatankus, as the native inhabitants called their little moon, and John hadn't been able to resist going up and doing a few not-so-approved maneuvers. Now on his way back to Central Command, his arms and legs were still tingling as his flight suit deflated once again.

John took the long way back, a dirt path that wound along the rear fence of the compound, but was shady and green from the tall ferns that grew along the marshes here. After today's dial-in, his next training flight wasn't until 1400, and except for paperwork, he was looking forward to a pretty easy day. And if he missed the pressure and excitement of his life from two years ago, it was better to just shove that out of his mind as soon as the thought occurred. 

A frantic lowing sound distracted him a second later, and he jogged around the corner of the building to find Cpl. Mannis poking a shock prod through the fence at a unacus—one of the local reptiles that looked like a cow with scales and had a peculiar, vertical jaw. It seemed like Mannis had discovered the unacus with its claw trapped and was tormenting the poor beast.

"Cut that shit out, Corporal," John said, stopping beside him. "Jesus, this is the second time you've pulled this crap."

"Sir!" Mannis had yanked the prod away and now stood at attention. 

"Don't just stand there—help it get its claw loose from the fence."

"Sir?"

"Don't worry; I'll keep it from biting you." The fences were meant to repel all predators on the moon—not that there were many—but the unaci were herbivores. Unfazed by the field, they often grazed right by it. 

John took the prod and turned off the power, then held the prong near the critter's vertical jaw, ready to push it back in case it wasn't happy with Mannis' help. Mannis bent down and lifted the wire just enough for the unacus to pull its foot free.

"Good. Now report to Sergeant Kim for non-judicial punishment, Corporal."

"Sir! Please..." Mannis' pale face was sweaty.

"Two strikes, Mannis," John said. "Article 134-1, Abuse of a public animal." John had made sure to look up the reg. 

"Yes, sir." After working his jaw for a moment, Mannis saluted and marched off, his shoulders stiff.

"Asshole," John muttered to himself and jogged back to Central. He was now going to be late for that cup of coffee he'd promised himself before the 1000 dial-in. 

"Kim," John said on the comm as soon as he reached his desk. "I'm sending Corporal Mannis your way. Caught him shock prodding a unacus out by the back fence."

_"Yes, sir. NJP?"_

"That's the plan."

_"If you don't mind my saying, sir, it's about time. He's had a word or two to say about having a tin man for a CO."_

"Yeah. Well, the tin man caught him red-handed this time, so even his daddy won't get him out of this one."

_"Copy that. Looking forward to the report."_

"I'll have it to you by this afternoon. Sheppard out."

John was just heading over to the coffeemaker when the Gate alarm sounded. With a sigh, he went back to his terminal. To his surprise, the connection didn't cut after the databurst. Instead, Commander Carter's face popped up on his vid screen.

John sat up straighter. "Commander. It's good to see you," he lied smoothly.

"Subcommander Sheppard," she said formally, making him tense further. "Atlantis has requested your reinstatement as princeps," she said, blunt words that punched him in the gut.

 _Hell with that,_ John thought. "Ma'am." He knew something in his expression must have betrayed him, because Carter's eyes softened. 

"John, this came from Atlantis itself. Not from the Intergalactic Committee or the Space Force." 

"Commander," John said, choosing his words carefully, "you know why I was deemed unfit to command. It's not like I've had a heart transplant in the last year."

"Nevertheless," Carter said. "Atlantis can have whatever pilot-captain it wishes. Commander Caldwell would still be CO of the troops."

"What happened to Caldwell's link?"

"I'm not privy to that information," Carter said, her mouth twisting wryly. "John, it's in the best interests of the SGCC that you accept."

John digested that for a moment. Of all the Ancient City-ships, Atlantis was the youngest and most bullheaded. It alone had allied with the Taur'i when the other City-ships had chosen princeps from Pegasus, even though their genes weren't as strong.

"You act like I have a choice. Aren't you just going to reassign me?" John couldn't help the bitterness. His last reassignment hadn't been voluntary either.

There was that wry smile again. "I don't have any personal experience, of course, but I'm told no one can force a link."

"No. That's true." Atlantis. It wanted him back, even if no one else there did. John's chest burned, and he could swear he felt his artificial heart whirring like an antique watch. "Fine. I have to wrap up my command here; I can't leave my guys on the lurch. Do you have someone to replace me?"

"Subcommander Mitchell will be taking your place until a permanent replacement can be found."

"Okay. He's a good Joe."

"Yup." Carter looked relieved. "He'll be through on the next burst." She smiled and nodded. "Thanks, John. And good luck. Carter out."

Four days. John had four days to get wrapped up here before handing over the reins. And then he was going back to Atlantis. 

Now he really needed that coffee.

:::

"So, I guess that's it, son," Mitchell said as he watched John pack.

"Make sure you keep the ball rolling on Mannis' proceedings," John said. "I want that guy off this base."

"Oh, he's toast," Mitchell said. "Anyone who'd want to hurt a unacus is no friend of mine."

John gave Mitchell a side-glance, pretty sure he was being ribbed, but Mitchell just grinned. "Seriously, though, they'll probably boot him from the SGCC for this."

"Good." John tossed his spit kit into his duffel and followed it with the last of his books. He wasn't sure what to do with his magazines but decided to just leave them for Mitchell and whoever would come after. They'd probably just drop them in the barracks. The rest of his exit checklist was completed; his squadron issued gear returned to the quartermaster; stunner, laser pistol, and crappy old P-90 returned to the armory; and medical paperwork dotted and signed. 

Mitchell took the seat at John's desk and put his feet up. "So, you're heading back to Pegasus." 

John had safely avoided any questions for the previous two days, but it looked like his luck had run out. "Been recalled."

"That a good thing?"

John shook his head. "Could go either way." True, John would be stuck in the middle of some seriously fucked up politics, but he still had an opportunity to prove something. 

Mitchell chuckled dryly. "You're a close-mouthed SOB, Sheppard."

"Yup." 

"Well, good flying," Mitchell said, and held out his hand. 

"Thanks. You, too. Take care of my crew."

"You got it." 

:::

On his arrival at Stargate Central Command, John reported first thing to the infirmary per SOP. But unlike standard procedure, Dr. Lam kept him on the table for a full examination of the very unique, life-saving tech presently embedded in his ribcage—the Ancient-built artificial heart keeping him alive.

It was weird, he had to admit, having her lay her hands on him and knowing she was communicating directly to his heart via the ATA; weirder still that he could sense the diagnostic commands she was feeding it and see the data she was getting in return.

`report[1]: *** [DIAG] QUERY 2: Function(FlowRate):`  
`>>return: *** [DATA] 10/lpm`  
`report[2]: *** [DIAG] QUERY 3: Function(ElecResp): `  
`>>return: *** [DATA] POS/++`  
`report[3]: *** [DIAG] QUERY 4: Function(BattLev): `  
`>>return: *** [DATA] 99.54% Cap`  
`report[4]: *** [DIAG] QUERY 5: Function(PortValveResp): `  
`>>return: *** [DATA] POS/++`  
`report[5]: *** [DIAG] QUERY 6: Function(Pulm): `  
`>>return: *** [DATA] 43.3 Sync `  
`report[6]: *** [DIAG] QUERY 1: Function(ReturnData): `  
`>>return: *** [DATA] Trans: Success`  
`...`  


"Any discomfort, dizziness, during strenuous activities?" Lam asked him, once she'd finished recording all the data.

"Nope. Actually, I'm beating my old times." John smirked. 

"Interesting," Lam said tonelessly. "Well, everything seems fine. Your battery is good to go for a thousand years or so."

John grimaced. He had to admit that part was weird—his new heart would keep beating long after the rest of his body, even his brain, was long dead. As long as there was blood in his system, it would tick away mindlessly. It would take someone with an ATA and the proper security code to shut it down forever. 

Of course, John wouldn't be around to care at that point.

"So, I'm good to go?"

Lam smiled briefly. "I'll have your paperwork ready for when you leave. When are you gating out?"

"Not sure. I still have to talk to the general."

Lam nodded and cut him loose. 

After putting his dress uniform back on, John's next stop was reporting in to the SGCC's CO, a meeting he wasn't looking forward to. Dr. Lam had made John something of a pet project after his injury, and her father, General Landry, had made it pretty clear he thought she was wasted too much of her time and energy on a "lost cause" when there were more important things she should be working on.

"Commander Sheppard reporting as ordered, sir," John said, saluting at the doorway of Landry's office.

"Sheppard." Landry waved him in, expression more affable than John had been expecting. "Carolyn get you all checked out?"

"Yes, sir. She says I'm in good shape."

"That's good. Good," Landry said, sounding like he meant it. "Have a seat."

John took the chair in front of Landry's desk and rested his hat on his knee. 

"Well." Landry leaned forward. "I suppose I don't need to tell you how critical your role will be in reestablishing this link with Atlantis. The City isn't too happy with us right now, Commander. We need to change that."

"I'm aware of the situation, General."

"Good. Good." Landry tapped his pen against his desk. "I realize you might have some lingering...dissatisfaction about being reassigned to the 306 project after being wounded. But policy is policy for a reason." 

John just waited. Beneath the desk, he clenched his hands together.

Landry cleared his throat. "However, we might have underestimated how attached each AI gets to the style of its particular pilot. Not that we think it will be necessary to relocate the City anytime soon," he added hastily, "but obviously there are everyday communications that must occur via the link between the City-ship and the command structure. I'm counting on you to be that link."

"Yes, sir," John said evenly.

"Good. That's very good," Landry said, and patted his hands on the desk. "Well, I'll let you be off. I don't know how closely you've been following things in Pegasus, but the war with the Grodari is enjoying something of a cease-fire, which makes this the perfect time for you to go back and get acclimated."

"Yes, sir. Am I leaving today?"

"As soon as you can."

"All right."

"Dismissed."

John left without a word, even though he wanted nothing more than to throw Landry's mealy-mouthed orders right back in his face.

:::

John spent the quarantine at Midway ignoring the puzzled looks from the new personnel transferring to Atlantis and the narrow-eyed, gossipy whispers of returning inhabitants by sitting in a corner of the mess hall and holding his tablet with a copy of _War and Peace_. 

He was trying to read, but instead all the junk he'd pushed to the corner of his mind came spilling out with a vengeance. The misery and pain of two years ago hit him right in the chest all over again, as if he were back on the table in the infirmary when Beckett told him what he'd done—what he'd had to do to save John's life—and the implications to John's future had made his new artificial heart jump into triple-digits.

At least it proved it worked properly.

And now he was going home. But it wouldn't be home any longer. Not when he didn't have any real place there. And not after that last, ugly conversation with Rodney. Hell, he didn't know if Rodney had even stayed on Atlantis—by the time they'd forced John back to Central Command, Rodney was still having trouble adjusting to the idea of his cybernetic eye prosthesis. John had communicated with Ford, Teyla, Radek, and the others, but once he'd heard Rodney had recovered physically, he'd avoided listening to rumors about his ex. 

John didn't want to think about Rodney.

He set his teeth and focused on the words of a man long dead.

:::

John waited until the other personnel had shuffled through the Gate before stepping through himself. The first sight that greeted him was Chief Director Woolsey, who finished welcoming the marine that had gone through before, then turned to smile at John.

"Commander Sheppard. Welcome back to Atlantis."

"Director," John said. He felt a similar welcoming nudge, restrained but pleased, push gently at the boundary of his thoughts. Polite—Atlantis had always been polite.

"If you'll come with me...?" Woolsey waved his hand. "Commander Caldwell and I would like to meet with you before you proceed to medical."

It was a little off protocol, but John agreed and left his bags beside the bottom of the stairs, giving a nod to the marine standing guard—LCpl. Dennison. John was glad to see he'd been promoted since John had left. Dennison came to attention but his face was blank, no recognition at all, and John felt chilled.

He caught up with Woolsey in his office. Commander Caldwell was a tall, balding bulldog of a man, with snub features and a barrel chest. John stopped at the doorway and saluted crisply.

"At ease, Commander," Caldwell said. "Have a seat. Director Woolsey and I were just discussing your place in the chain of command."

"And your duties," Woolsey was quick to add. "We're very grateful to have you back, Commander."

"Yes," Caldwell said, his mouth twisting. There was a story there, but Caldwell wasn't telling. Neither was Woolsey, but John didn't think it would be hard to find out the gist. "Let's be clear here, Sheppard: Atlantis needs a link to function. But despite what tradition says, your role will be princeps only. Due to your injuries, you won't be allowed on off-world missions or use of the jumpers, is that understood?"

John slouched a little in his seat and clenched a fist on his thigh. "Understood, sir."

"Now, regarding COC: I'm in command of this base and all personnel in it—"

"Well, insomuch as when there is a military situation," Woolsey put in. "This is, however, still a civilian outpost."

"But I think we can agree, with the Grodari being active and invariably hostile in this galaxy, that this is, in essence, a forward military base," Caldwell said, sounding like he was making a tired old argument. "Accordingly, chain of command includes civilians in certain situations."

"Certain situations, I agree," Woolsey said. "If only there were some way to open diplomatic relations with the Grodari—"

"Impossible," Caldwell said. 

John bit the inside of his cheek. Two years, and these two were still fighting over the sandbox.

"I hope you understand where you fit in, Commander," Caldwell said. 

"Right. I'm the pilot-captain and the link. No flying the jumpers, no ordering anyone around." 

Caldwell narrowed his eyes at John's tone, but he nodded abruptly. "Got it in one. I realize that might be a little difficult since this was once your command..."

"Not a problem," John said. His nails would dig straight through his palms at this rate.

"Then you are dismissed. Please proceed directly to the chair room after your medical." He paused and narrowed his eyes. "Problem?"

"No problem, sir," John said stiffly.

"Good. Report back after you've established a link."

"Yes, sir."

John got the hell out.

His bags had vanished by the time he got to the bottom of the stairs; he had to assume someone had taken them to his new quarters. He'd worry about them later, because right now he could feel Atlantis pressing against his mind like ringing a doorbell. Not insistently, but often enough that he knew it was anxious to speak to him.

"I'm coming," he muttered and picked up his pace to the infirmary. 

"Commander!" Dr. Keller exclaimed, delight in her voice. "What are you doing here?" Apparently, Woolsey and Caldwell had kept his return need-to-know. 

"Hey, Doc. I'm back. Not sure how long, but I'm here to pilot Atlantis." John shoved himself up onto an exam table and held out the chip with his medical records. "Process me in?" 

"Of course, of course." She took the chip and snapped it into her console. "I'd ask you how you've been, but I already know—I've been in touch with Dr. Lam." She shot him a glance between her lashes. "We worried, you know?"

"Oh. Thanks, but I'm—it's fine. I'm good. Beckett did good."

"He'll be glad to hear that." There was a double meaning there he really didn't want to unpack.

"He around?"

"No." She shook her head, wisps of hair falling around her face. "He's off on a medical relief mission for the Pegasus Alliance. We're in demand," she said, sounding a little defensive or smug. Maybe both.

"That's good." Maybe Atlantis was doing better these days. The other City-ships had been giving it the cold shoulder at Alliance meetings when he was Commander.

"Okay, let's get some blood."

John sighed and rolled up his sleeve.

:::

Medical cleared, his next stop was the chair room. He could sense Atlantis' eagerness glancing at the edge of his awareness as he headed to the nearest transporter, which was why he wasn't looking when the door opened and someone barreled out and nearly crashed into him.

"Hello, McKay," John said, recovering fast and planting a smirk on his face.

"You—Sheppard, what are you—well. If it isn't our ex-commander," Rodney said, a sneer lifting the corner of his mouth. "Come for a tour?"

John placed a hand on the wall. "Actually, I'm taking over as pilot. Atlantis requested it."

"Oh, really." Rodney paused just a moment, his blue eyes flickering as he processed the information. "Pity it didn't ask us for our input."

"I'm sure Atlantis already knows your opinion. You've never been shy about spouting it around."

Rodney sniffed. "You do realize this is probably just Atlantis' way of using the Taur'i to show up the other City-ships. You're nothing but a pawn in the game of Pegasus politics."

"Thanks. I got that," John said, gritting his teeth. "Maybe I'm playing my own game." 

Rodney narrowed his eyes.

"Anyway, got to go. Sure I'll be seeing you, McKay," John said, and palmed open the transporter. He made sure to have his smirk in place as the doors closed on Rodney's glare.

Damn it, it had taken Rodney ten seconds to get under John's skin enough for him to reveal more than he wanted to. Had to be a record. 

John felt an urgent flutter, a query, anxious and remorseful. Atlantis, obviously upset by the conversation. 

_I'm on my way,_ he projected, and tapped the quadrant for the base of the control tower.

As he walked the quiet corridor to the chair room, he let his fingers drift along the walls and his eyes rest on the tall, bubbling columns and the light fixtures, elegant and functional. He'd missed this place so much, too damned much to think about. 

The lights brightened under his fingertips, and he smiled involuntarily and walked a little faster.

But his steps slowed outside the doors to the chair room. Not that the chair was going to be a problem. Because it wasn't—this was why he was here. If he couldn't do this, he was sunk.

The doors opened. 

For a split second, his vision went hinky, and he saw smoke—smelled it—saw the chair burned and cracked, heard shouts of pain. 

John shook his head and approached the platform, halting at the base.

"With your permission," he said formally, phrasing it in his mind at the same time. 

The platform lit a friendly blue, and John took a deep breath and seated himself in the chair. Sweat tingled on the back of his neck.

There were words forming at the edge of his mind, inchoate but there—Atlantis was trying too hard to communicate with him. And as it happened sometimes, the gentle touch asking permission to link felt more feminine than neutral right now. He could never tell if it was his own imagining or Atlantis itself.

John nodded and said out loud, "You have my permission, Atlantis." He dug his fingers into the gel sensors.

He was expecting the rush of data, of Atlantis' overmind, but it had been so long the sensation was almost as powerful as the first time he had linked with her—the almost invasive push that thrust his own thoughts to the background until all he could hear was her.

 _[Commander Sheppard.]_ She rarely used words, but these two she did, sometimes, rarely, addressing him by his rank, unlike the other City-ships, who cared little for human hierarchies. 

"I hear you. It's good to be back," John said, relieved. He was past the critical point. They were linked. 

She expressed her gratitude for his return, a warm orange glow bright with sound and a bitter undertaste of guilt for his previous injuries. He could feel her rapid catalog of his vitals as a background patter, as if she were seeking reassurance he'd recovered fully. Also present was the dull purple throb of her remorse for dragging him back against his will. Her conflict of motivation was a dusty, burnished rust, an irritating sand against his skin, but when he tried to examine it further, reaching for the data, her stream went silent and black. When it returned, Atlantis felt once again neutral, genderless, calm, and made clear its desire to test the link.

"Ready when you are," John said, resigned to being kept in the dark for now. He reached for the cool blue stream it sent him and started investigating the City's systems.

:::

Afterward, John stopped by the mess for some coffee and grub. There were a lot of familiar faces, but many more unfamiliar ones. He was disappointed not to see either Ford or Teyla but relieved there was no sign of Rodney. John wasn't ready just yet for another dose of snide remarks.

"Hey, Corporal Sansome," John said to the lance corporal behind the counter. "What's good today?" 

"Nice to see you, Commander. We've got tava beans, refried tava beans on toast, and baked tava bean casserole," Sansome replied, his brown face twisting in a rueful smile. "But supplies came through today, so lunch should be better."

"Well, that's something." John had kind of missed tava beans, actually. "I'll have the casserole, thanks."

What he hadn't missed was the weird looks he got as he took his tray and searched for a table. For every Sansome there was a Dr. Gillespie, who kept staring at him as if his artificial heart was going to explode out of his chest on the spot; or a Lt. Greene, who apparently expected him to break into the Robot at any given second.

When he'd first arrived as CO on Tatankus, he'd gotten his fair share of looks, word of the Subcommander with the Ancient doohickey for a heart having arrived before him. But this was Atlantis. He realized he'd been expecting a more casual attitude from people who lived in the City of the Ancients. 

_Just goes to show,_ John thought, and picked at his lunch before giving up and bussing his tray.

He reported to Woolsey with coffee in hand and was surprised to find Caldwell in Woolsey's office again. Apparently those two were joined at the hip, either out of mutual suspicion or something else. From the way their heads were bent so closely together, it might be something else. Kind of an unexpected match, but in this galaxy, that happened a lot.

"Pilot-Captain Sheppard reporting as ordered," John said. "The link is complete." He kind of liked the sound of his new title, even if it was a demotion.

"That's good news, Pilot," Woolsey said, and then he reached under his desk and flipped the privacy switch. John blinked in surprise. Not that Woolsey didn't have a right to keep some communications private from Atlantis, but it sure explained some things.

"Then, Atlantis created a clear data channel?" Woolsey asked. "No obstructions?"

John frowned. "We ran through the usual tests. There are quite a few damaged areas that still need addressing; more than before I left, but obviously it was a rough landing." John winced a little at the reminder. Their last engagement with the Grodari and that rough landing had taken his command and Rodney's eye. 

"Yes, yes, of course. But Atlantis is happy with the link?"

John tilted his head. "I was told that's why it requested me."

Woolsey and Caldwell exchanged a glance that John couldn't decipher.

"Sir," John said, addressing Caldwell. "Atlantis was apologetic for pulling me from my previous post. But it also indicated a certain amount of urgency: in order to repair the damages, we'll need to relocate to a planet with an ocean rich in rubidium. And I mean a lot of it."

Again, Woolsey and Caldwell exchanged glances; this time, Caldwell looked almost angry, his lips pressing together.

John forged on with his report. "Atlantis conducted a survey, and the most suitable planets not in occupied Grodari territory would be P8W-681, P1F-539, or P5Q-563. All are uninhabited with temperate climates. Of all of them, P5Q-563 seemed the most suitable."

"I suppose it's only coincidence Atlantis never reported this to me," Caldwell said. "And that the first time it links up with you, you tell us you need to take it flying, when in fact you've been grounded for medical reasons."

John felt his face freeze in shock at the insult. He responded stiffly, "I am reporting verbatim. Sir."

Hard on John's heels, Woolsey said, "Steven, I've worked with John for years. I doubt he'd report false information."

 _Gee, thanks, Dick,_ John thought viciously. He said, as calmly as he could, "You're free to query a console. " For some reason, none of the City-ships liked stooping to communicate via terminal—either they felt it was beneath them, or they didn't trust the words were actually reaching the right humans, the anthropologists were unclear—but they would in emergency situations. Maybe Atlantis would be willing in order to get the rubidium it needed. 

"Maybe I will," said Caldwell, but Woolsey just shook his head. 

"File your report and we will take the information under advisement, Pilot Sheppard," Woolsey said, and waved his hand in dismissal.

:::

John figured asking LCpl. Dennison where his gear had run off to was as good a way as any to find out where he was bunked. He headed slowly down the stairs, a sense that he was being watched making him look around a little self-consciously. It shouldn't have surprised him when he found Rodney McKay staring at him, but somehow it did. 

Rodney immediately looked back down at his console, but snapped out, "Is there something you needed, Sheppard? Or are you just going to loiter in my control room like a lost lamb?"

"Actually," John drawled. "Maybe you could look up the location of my new quarters, if you aren't too busy." It was an absurd request, one that in the old days would have made McKay blow a nut about how he had far more important things to do with his precious brains.

But for some reason, Rodney smiled archly and said, "But of course. In fact, I'd be only too happy to show you to them, Commander."

"It's Pilot, now," John said, suspicious.

"Whatever." Rodney waved his hand. "Come along."

As they headed toward the transporter, John tried to ignore how natural it felt to be strolling side-by-side with Rodney through the halls of Atlantis. Of course, it helped that anger and bitterness were pulsing off Rodney in jagged little waves.

John blurted, "Are Teyla and Ford around?"

"They're on a diplomatic mission to Teleros. They should be back tomorrow," Rodney said. He waved open the transporter and hit a quadrant John wasn't familiar with. The doors opened, and Rodney gestured mockingly. "After you."

The corridor was dark but tried fitfully to light up as they walked. It smelled dank and unused down here, and John started to get a bad feeling. 

"New crew quarters down here?" he said gamely.

"Oh, no. I believe we opened this area just recently," Rodney said lightly.

Okay. Definitely a bad feeling. 

After a fairly long walk, during which John could feel his artificial heart beginning to thunk more rapidly with his growing anger, Rodney finally stopped before a nondescript doorway and passed his hand over the crystal. The door opened only grudgingly, and they stepped into a cramped, windowless room with a tiny bunk.

John's bags were lying on the center of the floor.

"Bathroom's down the hall," Rodney said, his voice gleeful. 

"McKay..." John started dangerously. Just then the lights flashed off and on, and the doors snapped back open behind them so fast they boomed within the frame. 

John leaned against the wall and gave Rodney a sardonic look. "I think Atlantis is countermanding your room requisition."

Rodney's mouth twisted. 

"You could go against Atlantis—" John halted when he felt Atlantis pressing against his mind, not subtly at all, and he granted its entry request. It let him know in no uncertain terms that it would not allow this disrespect of its princeps to go unchallenged. "—but it just told me pretty clearly that would piss it off. And seeing as the whole point of me being here is to get on its good side..."

"You look like an airhead when you do that," Rodney muttered, concession in his voice.

"Do what? Listen to Atlantis?"

"Yes." Rodney drew himself up. "You look like an empty-headed surfer rat." 

"Why, Rodney—you almost sound jealous."

"Hmmph." Rodney spun around and stalked out, throwing over his shoulder, "I'll see what I can do about finding you better quarters."

"You do that," John said, grinning. For a second there, it was almost like old times. He patted the wall. "Thanks, baby."

Atlantis hummed contentedly.

:::

John reported to the armory to get kitted with a stunner and laser pistol, and then the quartermaster for some other essentials. The laptop he'd been assigned by Sciences was a piece of crap, but John had kind of expected that. He still managed to hammer it into submission enough to pull up the server where all the form templates were stored, and he navigated his way through until he located the form he needed, PLR-20a, for a pilot link report. 

He first set out all the specifics of Atlantis' greeting, but avoided mentioning his personal perceptions, the gendered overtones or the synesthesia—he'd made that mistake once early on and he wasn't about to stir up the hornet's nest of creepily eager anthropologists and a worried Beckett wielding a CT-scanner. Not to mention McKay's derisive comments about delusional flyboys.

But the notes on rubidium would pique Rodney's interest, especially as it pertained to nanite manufacture. The increased nanites would not only repair the battle damages but would allow Atlantis to produce more drones and even replace lost puddlejumpers. 

John typed carefully, occasionally reaching out to Atlantis for details, until he had the report ship-shape. Then he saved it on the server and attached it in a mail to Caldwell and Woolsey, sending a separate mail to Rodney with nothing more in the body than the path to the report. 

Underhanded, maybe. But John hadn't spent the last two years elbowing for resources for his remote training outpost without learning a thing or two about gaming the system.

:::

Dinner just reinforced John's sense of solitude. He held his tray and took a look around; everyone was seated in clusters and chatting. He recognized faces here and there, but no one looked up, so he set his tray down on an empty table and dug into his stew with a vengeance.

"You! There you are." Another tray slammed down across from his own. He saw three packs of Jell-O on it and smirked to himself.

"Hello, Rodney."

"I got your report," Rodney said. "Thanks for the informative preamble, by the way—I see you've learned the value of brevity in your absence."

"Yup."

"Ha. So...nanites. And just why didn't Atlantis see fit to inform us it could manufacture more before now?"

John shrugged. "Who knows? We were kind of busy trying to stay alive back on P2V-181. Or maybe Atlantis wasn't that hard up."

"Well, first thing tomorrow, I want you to get back in the chair and ask Atlantis to pull up the specs on the nanites."

"Sure. You coming with?"

"No." 

The blunt refusal had John lifting his head to look at Rodney's face—much more closely than he'd been willing to since he'd gotten back. Rodney's lips were pressed in a thin line, his eyes refusing to meet John's. 

John found himself staring at Rodney's left eye, trying to see if he could spot a difference...there, he thought he caught the glint of optics, an opalescent sheen at the edge of Rodney's pupil. John's gaze wandered higher, to where the skin bonding had healed Rodney's burns but ended the hair growth halfway on his eyebrow, leaving him with a permanent, sardonic arch. 

"You haven't been back to the chair room since?" John asked, breaking the silence.

"Of course I have," Rodney scoffed. "Who do you think fixed the chair?"

"You just don't want to go back in there with me," John said, guessing.

Rodney dropped his knife and fork with a rattle and grabbed up his Jell-O cups. "I'll expect your report by tomorrow noon. If we're going to get any traction on this, we're going to need all the data we can get."

"Whatever you say." John stared after Rodney's retreating back.

:::

John had forgotten how cool Atlantis' showers were. No waiting for the water to heat up, just a perfect, warm rain from overhead under a calm blue light. Perfect for jacking off, too, except this morning he was still too on edge from the dream that awakened him. He'd been back in the chair, trapped, unable to move when the Grodari burst in with its weapon up and fired at the platform.

John woke up with Rodney's name caught in his throat.

"Fuck," John said, and waved off the water, reaching for his towel. In the mirror, he confronted the smooth, hairless skin of his chest. It had taken some getting used to, how the bonding had killed his hair follicles—well, a big enough patch that, self-conscious about it, John had gone ahead and had the rest removed. It still looked weird, enough that he avoided looking at his chest, or maybe it was just the thought of what lay underneath. 

John swiped his hand over the mirror to open the cabinet behind and get started with his day.

:::

Lunch was a turkey sandwich, limp greens, and Rodney spouting poetic over the nanite architecture. 

"They're multiphasic! They literally shape shift for their separate functions, repair versus manufacture," he gushed, fingers spraying bits of Fritos onto John's tray. 

"Cool." John sipped his coffee. "Hey, speaking of repair: did we ever figure out how that one ship penetrated the shield?"

Rodney's grin slid off his face. "Not as such."

"Well...that's kind of a problem, don't you think?" John had thought about it a lot, actually, late at night when he couldn't sleep for worrying about Atlantis. "What about introducing a randomized harmonic variance?"

Rodney stopped scowling and looked intrigued. "That's sort of brilliant. Did Atlantis come up with that?"

John glared, but Rodney was already moving on. "It's possible, if we introduce a shifting algorithm to...hmm. Definitely possible," he said around some Fritos.

"Well, work on it, why don't you?"

"You want me to work on introducing a randomized harmonic variance that would somehow be synchronized across all ten shield emitters—something obviously a little too complex for the Ancients to bother with—in between my other hundreds of projects?"

"Yeah. And make it snappy," John said, taking another bite of his sandwich.

Rodney gaped.

"Commander Sheppard?" Ford's voice called out behind him. John twisted around and then rose from his seat. Both Ford and Teyla were approaching, trays in hand.

"I knew I recognized that hair," Ford said, grinning. 

John returned the grin, saying, "Damn. It's good to see you two." 

"John." Teyla had a wide smile on her face. She put her tray down and took his elbows. John leaned in and touched his forehead to hers for a long moment, just breathing her scent, so glad to see her it hurt. God, he'd missed her. He'd missed them both. 

"Teyla. You doing okay?"

She laughed, a choked sound. "Yes, I am doing well." Her eyes were bright as she pulled away.

John grew aware of the bubble of silence around them, the stares they were attracting. "Well, let's sit down, catch up properly."

"Yes, let's. Hello, Rodney," she said, bending to pick up her tray and set it beside Rodney's. 

"Teyla. How went the talks?"

"Teleros still resists joining the Alliance. They fear it will make them targets of the Grodari."

"Damn. I hear they have advanced tech." 

Ford bumped in next to John and asked, "When did you get in? Are you visiting or what?"

"Yesterday, pretty early. Atlantis called me back as pilot."

"Whoa." Ford grinned widely. "Cool, sir." He ducked his head. "Hasn't been the same around here."

"That is wonderful news, John," Teyla said. "We heard nothing of it."

"Yeah. It was a surprise to me, too," John said. "But here I am."

"We must celebrate." Teyla looked at Rodney, something calculating in her expression. "Rodney, can you arrange for a TV night?"

"Oh-no, no way," Rodney said. "I'm a busy, busy, busy man."

"But I thought you wanted—ow!" Ford gave Teyla a reproachful look.

"No problem," John said. "Spar later, though?" He smiled at her winningly. "Just remember it's been a while."

"Yes, of course. I will try to be gentle." Her smile was wicked.

"And maybe we can hit the range," John said to Ford.

"Oh, yeah. Hey, you should try one of the new M249 plasma rifles we got in."

"It's a date." John looked over to find Rodney scowling at him, although he wasn't sure what for this time.

All he knew was this was his team. He had his team back, broken as it was.

:::

Yeah. This was a familiar view—the ceiling of the gym, and Teyla smirking down at him, her bangs plastered to her sweaty brow. 

John groaned and accepted the hand up.

"It's not as bad as it could be," she said encouragingly. "I noticed you didn't fall as awkwardly as you might have."

"You mean I didn't land on my head and break my neck?"

"Precisely." She grinned at him and raised her sticks. "Again."

"Yeah." John set himself for her attack, not surprised when he barely caught one blow out of three, the rest falling on his arms and shoulders. Still, it could be worse—he kept on his feet much longer this time and rapped one stick on her leg before she danced sideways and swept both feet out from under him.

He managed to throw his arms out to take the impact there first, and shouted his kiai so he wouldn't lose his breath.

"Good," she said. "Better." 

"Terrific." He panted a little, feeling the good ache. "Well, this was special. Thanks." He rolled to his feet and went to grab a towel. 

"How have you been, really?" she asked, sipping water, her towel around her neck. "Your mails dropped in frequency, and I worried."

"Well, you know. Not much to say. Same old, same old, every day. I was glad to hear about your promotion—" He pointed at her. "You got my present, right?"

"Yes, John," she said indulgently. "Although gifting a diplomat with a sword is a contradictory message." Her smile softened. "It was a lovely gift."

"Well. Nothing but the best for you." John found it on an Earthside trip in Japantown. He'd had to promise the storeowner the person he intended it for really knew how to use it. "You guys go offworld much?"

"Yes, of course. It grows more dangerous the larger the Alliance becomes—Aiden and I have been traveling to the very edges of Grodari territory."

"Wait—you and Ford alone? No McKay?"

"Aiden and I have a rotating team of marines who join us," Teyla said. "Rodney has not felt comfortable...he stays on Atlantis."

"Well, hell." That wasn't good. "Is his eye bugging him?"

Teyla frowned. "You will have to ask him, John. Now, tell me how you happened to return to us."

John knew a change of subject when he heard one, but it didn't pay to mess with Teyla. He cracked open a bottle of water and settled in to relay the important stuff, about the sudden recall from Carter and the Landry's anxious request. Maybe Teyla could shed some light on why Atlantis was using him as a chess piece.

He finished up with, "Atlantis felt guilty about dragging me back out here, but there was something else, as if it were keeping a secret. Do you know why Atlantis gave Caldwell the boot?"

Teyla pursed her lips. "I'm not sure, but it occurred shortly after the summit on Palanar when we met with the princeps of Helike, Akrotiri, and Amaya."

"Hmm. Thanks. And thanks for the bruises."

"Any time, John." She bowed with a smile.

:::

It was inevitable that John would run into his old XO, but he could have wished it wasn't at the range and surrounded by curious marines.

"Major." 

"Sir." Lorne cracked a wary smile. "I heard you were back. Looking good."

"Thanks. Good to be back." John looked around. "I see you made some improvements."

"Yeah. The commander requisitioned us some additional targeting equipment. Nothing too fancy."

Lorne was being diplomatic. The stuff was awesome—state of the art holographic pop-ups that looked damned life-like. 

"Hey, Ford."

"Sirs." Ford grinned. "You want to try out the new stuff?"

"Let's have at it. Good to see you, Major."

"You too, sir."

The new range was as terrific as advertised, and Ford's enthusiasm kept John from getting too bitter about it. They used their laser pistols to cap off Grodari, Goa'uld, and weird-looking predators, avoiding the odd civilian when they popped out, even if they were dressed as Genii. John had a tougher time with that than Ford, since John had once been captured by a Genii and tortured with a Grodari device in a fun little power coup.

"That was very cool," John said. "Wish we'd had a range like this at Tatankus."

"You haven't lost your eye, sir."

"Nice ass-kiss, Lieutenant," John said, and Ford smirked. "See you at dinner; I've got to go check in."

"Later, sir."

At his daily check-in, John dutifully reported that the nanite schematics had been delivered to the Chief Science Officer and filed on the server. 

"Atlantis has no other messages at present," John said.

Woolsey tapped his pen on his folder. "Atlantis seems determined to acquire these new nanites."

"Yes, sir. We've taken on too much damage for the present complement. They're just for maintenance."

"All right." Woolsey's lips tightened, and he stared beyond John's shoulder. "I'll see what I can do. Dismissed."

John turned and headed out the door, passing Caldwell on his way.

:::

It was only habit that took John's feet past the labs at the end of his jog. At least, that was what he told himself. It was at least partially true. He could have turned back at the end of the corridor, but he continued on and paused in the doorway.

Rodney was in full swing, his fingers stabbing the air as he jabbered at Zelenka, whose hair swam in a staticky cloud as he yammered back. Their voices ping-ponged against the glass window, making John grin.

Rodney's face was pink. The interrupted eyebrow made him look just a little surprised. It was charming, and John's heart tried to do something it couldn't possibly do anymore.

He knocked on the glass as he strolled inside, and Radek turned and then grinned. 

"John! It is good to see you, my friend." 

Behind Radek, Rodney's face creased into a frown. 

"Hey, Radek. How's the cheese experiment going?" 

"Not so successful, I'm afraid. Where did I leave you?"

"You were just going to try a paneer."

"Oh, no. Terrible. That was just terrible." Radek grinned maniacally, as if his failed cheese experiment was cause for hilarity. "Now the cheddar..."

"As amusing as this is, I believe we were working on something, Sheppard," Rodney cut in. "Make yourself scarce."

"Oh. But we must catch up later, Commander," Radek said.

"It's Pilot now, and sure, Radek. That would be great. You can tell me all about your cheddar." John made it sound dirty.

Rodney glared darkly.

John smirked and jogged away.

:::

That night, he dreamed again about the chair room. This time, the dream started after the battle on P2V-181, when they'd destroyed the last Grodari ship and decided to relocate to prevent a siege situation.

John had never flown Atlantis before and wasn't...nervous, really, just hyped; Rodney had plugged into the chair to assist. Atlantis was eager to fly, helping John stabilize as they left the ocean and then the atmosphere and entered hyperspace.

In the dream, John somehow already knew about the small Grodari fighter that had penetrated the shield and crashed into the main tower, causing so much damage that Atlantis itself was unaware of the squad of Grodari lying in wait. He tried to warn Rodney, but he couldn't; his throat was locked tight.

The Grodari were coming. Lorne had a team of marines fighting them back, but they were brutal, huge, and even multiple shots wouldn't put them down. One of them kept advancing toward the chair room, the clank of its boots in time with the thunking of John's heart.

His hands were frozen to the chair. It was going to happen all over again.

Atlantis had entered atmosphere on P3X-553 and was heading toward the landing site. John was focused utterly on the controls, on pitch and yaw and trajectory and bringing Atlantis as close to the target as possible before cutting the drive and engaging the EHD thrusters to soften the landing. He watched in clinical detachment as they reached the target, and then gave the command.

But dream John was yelling in his head to Rodney to _get out, get out now_ —and then it was too late, and the Grodari was at the door and firing its weapon at the platform.

Electricity slammed through John and his connection with Atlantis wavered; he felt a tremendous pain in his chest and heard Rodney screaming in agony beside him.

Then there was laser- and gunfire, and the smell of smoke and flesh burning, and the plaintive echo of Atlantis in John's head. He told it to cut the thrusters, and Atlantis dropped heavily into the ocean just as his heart stopped.

John woke up, his breath caught in his throat. 

He'd stopped having this dream a long time ago, and now he'd had it twice in as many days, and too vividly to be a regular dream. He rolled over and put a shaky hand on the wall.

_Atlantis. Why am I dreaming this?_

Atlantis sent him images of the Grodari walking through Atlantis; of Beckett and crew rushing in to help John and Rodney; of Beckett seeing the dead Grodari; of Beckett later doing an autopsy and removing the implant from the Grodari's skull and examining it with a probe.

_So, you know something about them? Something that will help us?_

Atlantis gave him a wash of ambivalent pink, sweet and sour on his tongue. 

_Okay, then._ John blew out a frustrated breath. _No more dreams, all right? I need my beauty sleep._

He got an affirmative, clear and blue.

:::

John got an email from Jennifer Keller to stop in for a Pegasus flu shot, so he swung by after breakfast only to find the infirmary buzzing with excitement.

Marie tore herself away from the pack of nurses and had him sit down on a gurney, where she started prepping the shot. 

"What's up?" John asked her. 

"Dr. Beckett is back," Marie said, her face lighting up with a smile. "Please roll up your sleeve."

John yanked his sleeve up over his shoulder. "Hey, cool. I'd really like to—"

"John! I just heard the news, and here you are, lad." Carson's familiar accent had John turning his head just as Marie stabbed him.

"Ow!" John said, hamming it up. Marie smiled again, unusual for her. "Hey, Doc. Just getting the usual roughing up here by your wonderful staff."

"Oh, yes. I trained them well," Carson said proudly, coming up beside her. "It's good to see you, son. And looking so well." 

"Thanks to you, Carson."

"Ah, well." He nodded at Marie, who gathered her tray and slipped off. "It was something of a Hail Mary, to be quite frank. We both lucked out."

"I never got a chance to thank you, though. So...thanks." John had been too crushed by pain and resentment to thank Carson properly at the time. 

Carson patted his leg. "None of that. Come, let's go to my office and have a proper reunion."

That was how they ended up pulling the bottle of 18 year-old Glenfiddich from Carson's drawer and toasting Carson's successful relief mission and John's reinstatement on Atlantis. 

"How has Rodney taken the news?" Carson asked, pouring John another shot.

"By hacking the housing assignments to give me quarters in a dungeon."

Carson chortled. "Aye. That's our boy."

John wanted to protest that Rodney wasn't his anymore; that was the whole problem. Maybe the scotch was making him a little maudlin. He didn't get the chance, though, because speak of the devil, he saw the man himself come trudging into the infirmary and straight toward Carson's office.

"Carson! Carson, I heard you were back. Why haven't you—oh. Oh, of course," Rodney said, his voice dripping sarcasm. His eyes took in the scene. "Drinking at noon? Well, I suppose those of us without real jobs can afford to."

That stung. "Hey, Rodney," John said, waving. "Pull up a crate."

"I just got back half an hour ago, Rodney," Carson said. "I haven't even unpacked."

"But you have had time to get chatty with Commander Laze-a-lot, whose only responsibilities are to mind meld with an AI and _steal all my friends,_ " Rodney thundered.

John looked at Carson, whose eyes had gone wide. "All right. I'm just going to go meet with my staff. You two," he waved between them, "have a drink and sort this out like gentlemen." Carson ran like a coward, closing the door behind him.

John poured Rodney a knock and then sat back. It looked like they were finally going to hash it out. "Somehow, I'm flashing back to my divorce proceedings. Listen, you can take the fondue pot and I'll keep the leather ottoman."

"Very funny." Rodney took the shot but didn't drink. "They're _my_ friends, Sheppard. Mine. You left, remember?"

"Jesus. You say that like I had any choice."

"I gave you the option to stay as a civilian consultant; you just didn't want it." Rodney drank his shot, making a face.

John stared in furious disbelief. "Right! Let's not forget that winning move, where I give up my entire fucking career just to play lab monkey all day long."

Rodney's mouth moved before he sputtered, "Your career! You mean getting shot at—"

"Oh, nice. And don't forget my pension. And I'd have given up any chance at flying. Just to get to see you, what? Four or six hours a day? Tops? While you slept?" 

Rodney had the grace to look abashed. "I would have made time."

John snorted.

"At least you would have been living in the same galaxy!"

"Right. You'd be doing the real work while I'd be sitting around with my thumb up my ass waiting to spend time with you. You call that a life?"

Rodney's voice was choked. "Well, I'm sorry. Maybe it was hard to think up a good alternative when half my face had been burned off. Did that ever occur to you?" 

No. It hadn't, because John had been lying flat on his back, his career in ruins, his body mutilated, Atlantis slipping out of his hands, and Rodney with it. "Point," he said.

"Carson had just finished surgery on me, I had a brand-new eye that wasn't mine, and there you were, lying there—" Rodney cut himself off and grabbed for the bottle. 

John's fury deflated, and he took a sip of scotch to calm himself further. "Okay, so maybe we both weren't in good enough shape to talk about things."

Rodney stared down at his hands and nodded abruptly. 

"I needed to keep flying, Rodney." 

"I don't see how you thought that was possible, considering the rules were—"

"I made it happen."

Rodney looked up, his eyes narrowing.

"I started out doing back-up on training flights. By the time I'd been there long enough for them to get used to the old man, no one said a peep when I started taking the new ships up solo for shake downs." John shrugged. "It was my command."

"Oh. Well, I'm glad," Rodney said grudgingly.

"How's the, uh, eye working out?"

"Well, you know. Sometimes it gives me excruciating headaches, which Carson insists means I'm resisting integration or some such mumbo-jumbo. I'm not on anti-rejection medication any longer. I have found it useful on occasion in analyzing frequencies beyond the human spectrum." Rodney bit his lower lip. "Carson says with more practice my capabilities would be pretty much limitless. I haven't found the time, of course."

"Of course."

"So..."

"So." They sat in silence for a minute, then John capped the bottle. "Maybe you aren't the one I was really mad at."

Rodney gave a grudging nod. "It's possible my anger was slightly misdirected, it being an impossible situation to begin with."

John bit his lower lip. "Are we cool?"

"You're cool; I'm fine. But, just so you know..." Rodney lifted his chin. "I'm seeing someone."

"Oh?" John's stomach tightened.

"Well, not seeing so much as...we've had coffee twice. She's very nice. A botanist."

"'She,'" John repeated, relieved. "Good luck with that." 

Rodney scowled.

"But you and I are cool, right? Like, if I said TV night tonight, let's watch some original Trek with Ford and Teyla?"

Rodney regarded him for a long time, then grabbed the bottle from John's hand and poured himself another shot of whiskey, tossing it back clean. 

"Sure," he said morosely. "Why not?"

:::

To John's surprise, Rodney did show up for TV night bearing a remastered, HD version of the original Star Trek series so they wouldn't have to watch "that fuzzy, low-rez crap on the shared server." 

"And don't get me started on the missing scenes," Rodney griped, bending over to connect his laptop to the flat panel in the rec room. John watched Rodney's thighs flexing in his baggy BDU pants and sighed to himself. 

"Now," Rodney said. "We're starting with _Amok Time,_ written by Ted Sturgeon. He really had a feel for the characters, and for how truly different Vulcan society was from human." 

"Chekov and Sulu were pretty funny in this," John put in from hazy memory.

"No...spoilers, please," Teyla said. "Or do you not want popcorn?"

They all shut up and settled in to watch. Rodney had chosen to sit next to Teyla, which left John on the chair next to Ford. That was fine. They still kibitzed across at each other about the crappy sets—Spock smashing the monitor in one blow was pretty funny—and Rodney had a word or two to say about the distances involved in traveling across the galaxy versus the velocities represented by the various warp speeds. Everyone quieted down, though, when Kirk gave his speech about countermanding orders to get Spock to Vulcan in time to save his life.

_"I owe him my life a dozen times over. Isn't that worth a career? He's my friend."_

Cute, John thought. Really cute, Rodney. But afterward? If things hadn't worked out the way they did, Spock and Kirk would never have seen each other again. 

And if Rodney's life were in danger, it wasn't like John wouldn't willingly throw his career away to save him. Those hadn't been the stakes. John gritted his teeth and watched the rest of the show, but he'd lost his taste for wisecracking. He could tell Teyla and Ford had caught the vibe and were trying to pick up the slack, but it was heavy going.

Rodney didn't say a word until the final scene, when Spock explained that, after he thought he'd killed Kirk, he'd lost all interest in T'Pring. Rodney snorted and said, "Even when I was a child, I thought there was something hinky about that."

John smiled a little. He remembered watching it and wishing he had a friend like that.

"Thank you for hosting us," Teyla said as Rodney disconnected his laptop. "I'm glad we will be having TV night again." 

"Yeah. That was pretty cool for a cheesy show," Ford said.

God, he made John feel old. But _Star Trek_ 's popularity had, in a strange way, paved the way for many new technologies to be developed, such as the hypo spray, skin and bone bonding, laser surgery, stun pistols, laser guns, and EHD drives on commercial aircraft.

"Next time, Teyla picks the show," John said, and she nodded, smiling secretively.

Rodney scowled.

:::

The days settled into a routine of checking in with Atlantis, reporting to Woolsey and Caldwell, meeting up with Teyla and Ford for lunch and dinner, and occasionally radioing Rodney to request a manual repair.

That was fun. Rodney was gruff and pissy, showing up twenty minutes late with a travel mug full of coffee and carrying a toolbox. 

"What is it this time?"

"You didn't read your email?"

"I didn't bother, considering the wild goose chase Atlantis sent us on two days ago."

"Hey, you said yourself that conduit was hinky," John defended Atlantis, who was sounding distinctly masculine and more than a little ruffled in his head.

"Yes, but couldn't Atlantis have directed us right to the problem area, instead of having us squirming through miles of Jefferies tubes? Honestly. And why send me instead of Zelenka? He loves that kind of thing." Rodney eyed him over the lip of his mug. "Unless you made a substitution in the request."

John ground his teeth together and rounded on him.

"Sorry! Sorry," Rodney said, raising his free hand. "I know you wouldn't do that."

"Never," John said. "As in, not ever."

"I know." Rodney sounded contrite. "And I know it's a tremendous insult to imply a pilot would do such a thing, so you don't have to call me out on it. Sometimes my mouth runs ahead of me."

"Sometimes?" John raised an eyebrow.

Rodney's grimace conceded the point. "So what's on the docket for today?"

A truce appeared to have been called, because Rodney seemed almost chipper as he listened to the run-down on the sensor failure. 

"Could be damage from the original crash that's just surfacing now. Let's go."

John took Rodney to the problem area near the base of the central tower. Atlantis had complained of three cameras being non-functional and its sensors working only sporadically in the corridor. Rodney put down his toolbox and opened it to select the crazy-looking spanner wrench that was used to open Atlantis' junction boxes.

"Oh, now look at this—" Rodney had cracked open a box at shoulder height and was prying inside with a plastic probe. John had let his eyes drift away from the bunching of Rodney's shoulder muscles, only to drag them back when Rodney exclaimed, "Ha!" He tossed something, and John caught it automatically.

It was a half-melted slug. Probably from a P-90. "Now that would explain a lot," John said.

"Why your idiotic military still relies on projectiles is beyond me. The nanites had grown the repairs right around it," Rodney said. "The metal from the slug shorted out the connection. I'll need a new D5 crystal—get me one from my toolbox." 

John knelt down and sorted through the neatly packed crystals until he found one labeled 'D5.' He unwrapped it and offered it to Rodney, but he just shrugged his shoulder.

"You slot it in; I'm holding the wires out of the way."

John leaned over Rodney's shoulder and tried to fit the crystal into the slot. It would take a little maneuvering—the niche was tight and it was hard to see. 

"Too dark," John said.

"To your left. Little more...now up."

Rodney must have been using the night vision of his prosthetic. John was conscious of his chest pressing up against Rodney's back, of Rodney's warmth and scent as he leaned closer and clicked the crystal into place.

"There," Rodney said, sounding a little breathless. "That should do it."

Atlantis gave John the affirmative. "Atlantis is sending me images from all the cameras. Sensors are picking us up, too."

"Oh, you can—that's very..." Rodney shivered slightly and pushed back against him. 

John pulled away reluctantly. 

When Rodney turned, his eyes were thoughtful. "Well. On to the next, I suppose."

John nodded, feeling hope for the first time in a long time.

They spent the afternoon doing repairs and making jokes, sometimes inappropriate ones. While Rodney was adjusting the flow control for the master septic pump, John interrupted a string of plumber's crack jokes that was going nowhere good to ask Rodney if he'd worked out the shield problem. 

"In my copious free time, you mean?" But there was a smirk on Rodney's face.

"You're saying you cracked it? Not a pun," John added hastily.

Rodney's smile widened. "Yes, actually. I have it running in a sim at the moment. Of course, we'd have to implement it in all ten of the shield emitters and then synchronize them with the shield up. But I'm sure will work. Well, 98 percent sure, which for most people—"

John squeezed his shoulder. "That's terrific, Rodney. Awesome."

"Yes, well," Rodney ducked his head. "It's no drain snake."

John laughed.

"Of course, if it were, mine would be bigger," Rodney said slyly.

That deserved a slap on the head. John changed it mid-air to a tap on the cheek, and when Rodney just grinned, John smiled back.

Maybe it was okay to hope a little. 

:::

"Thank you for coming, Pilot," Woolsey said, shooting a look toward Caldwell. "I've—that is we've—given the matter of relocation due attention and would like to proceed, with some questions and caveats to work out with Atlantis."

John nodded and pushed his chair back so he could lean his shoulder against the wall. "Go ahead."

Woolsey looked surprised; Caldwell, skeptical. 

"Is that—are you in contact?" Woolsey said. John had to wonder how poor Caldwell's connection had been to the City.

"Yes, sir."

"All right then. Regarding P5Q-563: it appears to be located rather close to Grodari territory."

John queried Atlantis, who popped up a map on the projector screen, showing known Grodari territory and highlighting the location of P5Q-563. Something about the map pinged John's spatial radar, and he studied it a moment longer before turning toward Woolsey.

"It's closer than I'd like, but not that close."

"It's fine," Caldwell said shortly. John and Woolsey exchanged a look.

"I'm not sure—" 

"Enough. If we're going to do this, let's not pussyfoot around." Caldwell jerked his chin at John. "Let's be clear about one thing, Sheppard—you aren't officially cleared to fly. That said, I understand Atlantis will probably prefer its primary pilot to do the honors."

"Yes, sir," John said, holding back his anger by pure effort. Atlantis was chiming frantically in his head. _Don't worry. Nobody is flying you but me._

"You will have Major Lorne available as back-up."

"Affirmative. Also, sirs: Dr. McKay has been working on adapting the shield. We should make sure those changes are in place before making the move."

"I saw something about that in a memo," Woolsey said vaguely. He penned himself a note. "I'll look into it."

"Is that all?" John was eager to get to the chair and talk to Atlantis directly. 

"Dismissed."

John went down to the chair room, an uneasy feeling growing in the pit of his stomach. That map. Something about that map, and now all the pieces were bumping against each other in his head, like a jigsaw puzzle where the edges didn't quite match.

John sat down in the chair. _Atlantis, bring up that map again._

The map of Grodari territory popped into his mind, this time in three dimensions, which was all he needed to see what was missing. It was crude, with some vertices blank, but it was there: the rough outline of a dodecahedron floating in space. 

Why? 

_This is what they're after._

Atlantis sent an affirmative.

_If only we could communicate with them somehow._

A flurry of images/tastes/colors flashed across John's mind, Atlantis at its most excited, far too manic for John to process at once, but he caught the gist: the Grodari implant, Caldwell, a spate of red/anger, and the summit on Palanar.

_You told Caldwell you could communicate with the Grodari. You wanted him to tell the other City-ships, and he broke the Pilot code._

_[Yes, Commander Sheppard.]_

John's temples throbbed. _You think we can negotiate peace with the Grodari._

_[Yes, Commander Sheppard.]_

Oh, God. This was huge. And terrifying. Why had Caldwell broken the code? Why had he held back such vital information? 

Atlantis had been understandably hesitant to trust another princeps but had called for John, hoping he, at least, would be willing to listen. 

And now, even if it could lose him everything all over again, John's duty was clear. 

_We have to call another summit._

Atlantis' gratitude washed over him, almost swamping him. He soothed it for a moment, then said, _We have to be careful, though. I don't understand what Caldwell is up to. Let's get you to P5Q-563 and fixed up. Once I've flown you, I'll have more pull as Pilot. Then I can call for a convocation._

Atlantis sent the affirmative. It also sent an apology for deceiving him.

John sent wordless reassurances back, still overwhelmed by the knowledge they could communicate with the Grodari. But how?

Turned out Atlantis had some ideas about that, as well.

:::

"Hey, Rodney."

"What? Oh, Sheppard." Rodney looked over from his monitor and gave him a faint smile before turning back. "Yes, yes. I'm working on the emitter problem, actually, so you came at a good time."

"Really? Cool."

"I've got them syncing up properly in simulation, but there's something not quite—I can't put my finger on it—but the sims have run successfully a hundred times now under different scenarios, so maybe I'm just being paranoid." 

"'Paranoid is good. Paranoid saves lives.'"

"Now you're quoting me. Are you sucking up for some reason in particular?"

"Yeah, actually. Special project. Very hush-hush."

"Oh, another special project." But Rodney didn't sound all that put out; in fact, he was smirking at John indulgently. John's neck heated up, and he reached into his pocket for the box he'd lifted from Carson's lab. 

"I need you to take a look at this and make me a device that will input and output on the same frequency. It has these receptors..."

Rodney had frozen and was staring at the Grodari implant inside the clear plastic box. "Is that what I think it is?"

"Yeah." John cleared his throat. "Sorry. I know there are some bad memories—"

"Bad memories." Rodney's voice cracked. "Bad memories." 

"I-I know, Rodney." Jesus, he should've thought this through. He squeezed Rodney's shoulder. "But if we could stop—Rodney, we might be able to stop the war."

"What? What's that?" Rodney looked like he was coming out of a fog. "How?" He sat down heavily and put the box on his desk. "Why are you always doing this to me, Sheppard? Seriously."

"It's not me." John crossed his arms. "Atlantis gave this information to Caldwell before the summit, but he refused to pass it on."

"Yes, well. Caldwell has been acting really weird. It seems like all he's interested in is tech acquisition, which makes sense on one hand—we are fighting a war—but it's strange. He keeps sending Teyla and Ford out on diplomatic missions to tech-heavy planets and then hoarding the samples instead of passing them on to the science department. I'm not sure what kind of weapon he's looking for—what?"

John stared at Rodney in alarm. 

"What? So what was it about the device?" 

John shook his head. "Atlantis has translated the communications it recorded when we were invaded. This was the first time a City-ship was in direct contact with one of the Grodari, thanks to them penetrating the shield. It analyzed the device, and thinks if you can make a transmitter/receiver, we can communicate directly, with Atlantis translating."

"So? What will that gain us? They've made it pretty clear what they're after."

"Yeah, they have. Look." John put his hand on Rodney's monitor and asked Atlantis to project the three-dimensional map on the screen, then traced the vertices with his fingers. "This is what they're after for some reason. As soon as they capture a vertex, they stop their aggression in that quadrant. We just didn't put the pieces together."

"You think if we offer them bases in each vertex, they will calm the hell down."

"Yeah. Atlantis says they're a hive mind. They should reach consensus pretty fast if we offer them a treaty."

Rodney tapped his chin. "It's worth looking into."

"Look fast. We're leaving for P5Q-563 in five days."

"Sure. I'll just throw it in there between reprogramming all ten shield emitters." Rodney's voice dripped sarcasm.

"I can help with that."

"Oh, you will." But Rodney's smile was fond, and John couldn't help flushing warm all the way through.

:::

As promised, Rodney handed him a clunky-looking device the day before take off. It was about the size of a life signs detector but much heavier. John added it to his gear.

He'd helped Rodney with the emitters, but was no closer to solving his own problem: figuring out what to do about Caldwell. John had his suspicions, but bringing them to Woolsey would be a delicate matter for more than one reason. Commander Caldwell's record before being assigned to Atlantis was impeccable; he was the very model of a Taur'i Star Force officer. Somehow, after getting his orders and becoming Atlantis' military commander, he'd turned into a war mongering tech junkie. 

The pieces fit too neatly. And Atlantis was at risk. John would have to make his move, and damn the consequences.

:::

"Teyla, Ford, I need a favor," John said at dinner the night before the launch. 

"Anything, John. You know that," Teyla said, and Ford added, "Of course, sir." 

John nodded his gratitude.

:::

"You sure you're okay with this?" John asked Rodney, who seemed to be taking way too long setting up his laptop, his fingers fumbling with the cables. "I bet Zelenka would be happy to co-pilot this time around."

"I'm fine—just fine," Rodney said. "Who else can be trusted to keep you from crashing us into a sun or possibly getting us sucked into a black hole?"

"There's that can-do spirit, Rodney." John patted Rodney's head and got swatted for his troubles. "I'd rather have you, anyway," he added truthfully, and Rodney's face crinkled smugly, his nervousness forgotten.

"Of course you would. Now sit down."

John sat in the chair, and Atlantis reached for him immediately, their mutual excitement at the idea of taking flight flooding between them, sharp and crisp like a New England apple.

"Oh, I've missed this," John murmured as he waited for take-off. He could feel the whir of his heartbeat, strong and true, and the clarity of adrenaline in his veins. He opened his eyes to see Rodney looking at him, a wry expression on his face.

"I knew that, of course."

"What?"

"That this was at least half the equation of John Sheppard. I just...I don't think you realized how awful it was, seeing you half-dead in that infirmary bed, hooked up to God knows what. Your heart died, John."

"God. Rodney—" John's radio chirped. "Damn it," he said under his breath, and tagged the on switch. "Sheppard here."

"Pilot, Control is ready. You are a go for launch on your countdown."

"Affirmative. Dr. McKay is finishing pre-flight." John gave Rodney an apologetic look.

"Right. Well, work intrudes, as ever," Rodney said, and went back to his post at John's shoulder.

_Atlantis, are you ready?_

Atlantis sent back the pre-flight checklist, systems green down the row.

"We're good on all systems," Rodney echoed. "Zelenka is monitoring output from the ZPM room." 

John sank his fingers into the gel pads. "Attention all personnel. This is Pilot Sheppard. We are go for launch in one minute. All hands make flight ready and secure to posts." _Atlantis, start the clock. And make sure all the damned windows are closed._ Last time they'd lost more than a few to shudder shock.

Major Lorne dashed through the door and hastily unclipped his P-90 before strapping himself into a chair next to Rodney.

"Good to see you, Major."

John watched the readout in his head and warmed the star drive at the thirty-second mark. Atlantis rumbled to life beneath him, singing through his bones.

"Rodney. Shields."

"Done."

 _This is it._ "Taking off in 10...9...8...7...6...5...4...3...2...1..." He closed his eyes and went for the burn, felt Atlantis' glow, fierce and eager as she wrenched herself from the pull of the ocean and leapt skyward, now faster, pushing herself through the thinning blue of the atmosphere until she was free, free. God, what a rush.

"We are extra-atmospheric. Plotting hyperspace solution." _Atlantis, give Rodney the goods._

Atlantis, cool and neutral once again, sent back an almost amused affirmative and gave him the solution as well. It looked like close to six hours in hyperspace followed by a slowing forty-five minute trajectory within the new solar system. 

"Looks good," Rodney said. "At least I can trust Atlantis not to steer us into any dwarf binaries. I've input the solution."

John spoke into his radio. "Entering hyperspace. Approximately six hours to the P5Q-563 system." He triggered the drive and felt the slight shudder as Atlantis went hyper. John clicked off his radio and stretched his shoulders. "Cool."

"Oh, yes. Very cool." Rodney made a snapping noise. "Major, why don't you go get us some coffee."

"Gee, McKay. Shine your shoes while I'm at it?"

"No. Just coffee will do."

John cracked open his eyes and nodded at Lorne. "If you don't mind, Major." 

Lorne looked a little mollified and nodded back. "All right. Guess we could use some snacks for the trip." He sauntered off, Atlantis obligingly opening the door for him.

"Thank God," Rodney said. "Now, where were we?"

"Before we blasted off into space?"

Rodney waved his hands. "Yes, before all that."

"Rodney, I..." John squirmed, trying to get comfortable. "Hang on a second." His tac vest was way too bulky for a six hour trip, and he removed a couple of things from his pockets—his heavy-duty flashlight, a couple of packs of C-4, his spare knife in its sheath, and the Grodari translator—and set them beside his leg on the chair.

Rodney stared at him as if he were a little buggy.

"Sorry," John said. "Um. You were saying how fucked up everything was. And I was going to tell you...to tell you..." He thought back to those days, of lying in the infirmary trying to escape the unfamiliar rhythm of his unnatural heart, as if he could climb right out of his skin and back into the past. But he couldn't. He was losing everything, his command, Atlantis' warm touch, flying, combat, his family here. 

Now that there was a chance he might lose it all over again, he could finally say it. "Of everything I was losing, the worst part was they were making me leave you."

Rodney moved closer, his eyes going wide, so wide the light glanced against his prosthetic and John could clearly see the opalescent sheen of delicate machinery behind his pupil. Then he blinked and it was gone. 

Rodney said slowly, "And, of course, I wanted you to lose even more to make you stay."

"Well, yeah."

"But only because I couldn't bear the thought of you dying without me somewhere out there in the Milky Way. I even wondered why you didn't ask me to come with you."

"What?" John's throat went tight.

"Well, why not? It's not like I'm not welcome wherever I go. I'm brilliant." 

"But you—Atlantis." 

"Yes. So?" Rodney lifted his chin.

"I couldn't ask you to do that."

Rodney smiled and leaned over him. "Well, of course not. There's only room for one selfish bastard in this relationship. Admit it—you have feelings for me. Deep, devoted, might I say passionate—"

John yanked him down for a kiss. Finally, God, finally. It was awkward—Rodney's hands flailed and then rested against John's shoulder and chest, and he accidentally bit John's lip, but John had to count it among his favorite kisses ever, because Rodney was grinning against his mouth, little puffs of delighted laughter grazing John's lips. And Atlantis was sending confused but happy signals into John's brain—they'd never kissed in the chair before, and Atlantis wasn't sure what to make of it.

"So I guess this means things didn't work out with that botanist," John murmured.

"What botanist?" Rodney smirked and then sucked on John's lower lip.

Just then, the chair room doors slid open. "Jeez. I thought you two broke up," Lorne said.

Rodney groaned and pulled back. "Not that it's any of your business, Major. But we did—are. Or aren't." He gave John an uncertain look, and John said quickly, "Not anymore."

"Congratulations then, sir. I think."

"Oh, shut up," Rodney growled. "Did you bring any sandwiches?"

John laughed.

:::

The trip through hyperspace went smoothly. Thanks to Lorne's presence, they couldn't discuss anything personal, but John was grateful for that. He'd kind of exceeded his quota for talking for the next ten years or so.

Instead, Rodney pulled up some word games on his laptop and proceeded to smear them both. Lorne retaliated by insisting on a round of "Who am I?" and picked an obscure Goa'uld from the war. John did okay in the next round by selecting Sammy Davis, Jr.—he had them both stumped for a long time. John won Rodney's round by guessing 'Samantha Carter' in four questions, making him pout.

At the E-minus five-minute mark, Atlantis gave John a ping, and John keyed his radio. "Attention all personnel. Five minutes until we exit hyperspace. All personnel secure to posts." He keyed off and started stuffing his gear back in his pockets. By his elbow, he heard Rodney and Lorne giving quiet instructions to their staff.

At the one-minute mark, he gave another warning and then nudged Atlantis.

_Ready to see your new home?_

Atlantis evinced excitement and a little...not fear, but concern. John knew Atlantis had picked P5Q-563 because it was located at one of the vertices of the dodecahedron, but was still unoccupied space. It wasn't much of a risk: they could always tank up on rubidium and then leave if the Grodari started encroaching on the system. 

_Do you know something I don't?_

Atlantis signaled uncertainty.

Too late, though. It was time to leave hyperspace. 

"Exiting hyperspace in 5...4...3...2...1..." He shut down the drive and keyed off his radio. 

John's first view of the system was beautiful from Atlantis' perspective—13 planets, three of them with rings, and a yellow dwarf pulsing quietly at the center. And then John's view shifted, zooming in and then zooming again on the fourth planet, P5Q-563, and the Grodari ships circling it. 

"Well, fuck," John said. "Rodney, tell me your shield variance system is in place."

"Why? Oh. Oh, this isn't good." 

John decelerated and hit his radio. "Atlantis, all hands. All hands, we have Grodari in the system. Prepare battle stations."

_"Sheppard, this is Caldwell. Report!"_

"Commander. So far they don't appear to have seen us. We have the option of flight. They are centered around P5Q-563."

_"Understood. Senior Staff will consult. Major Lorne, stay at your station."_

"Yes, sir." Lorne said. 

John knew what that meant. Caldwell would boot John out of the chair in a combat situation. It burned, especially since Caldwell didn't know John had flown an F-306 in combat back on Tatankus to repel a Goa'uld attack. Of course, John had fudged the AAR to make it look like he'd coordinated the defense from the command post, or it would have been his ass in a sling, victory or not.

Atlantis buzzed in John's mind. This could be the opportunity, Atlantis was telling him. They just had to capture one Grodari and communicate with it.

_Easier said than done._

The City-ship hovered at the edge of the solar system, waiting for Command to make a decision.

"This is crazy," Rodney said nervously. "The longer we sit here, the more likely they'll notice us and attack. Their sensors are easily up to the task." John understood Rodney's concern; they'd been here before—right here, in fact—the only difference being they knew what was coming this time.

An instant later, a wash of red splashed against John's mind. Atlantis' shield had been hit, and from an unexpected quarter. Some ship returning to the quadrant, maybe.

"A hit on the shield," John said, sending through the radio, "Commander, we've been hit."

_"We're aware of that. Major Lorne, take the chair."_

Atlantis protested in John's mind, but John soothed her with the thought—he could do much more if he were mobile. Lorne could handle the drones. 

Atlantis let him go, and John stood, more reluctantly than he'd let on. It hurt to leave Atlantis, to relinquish control. 

"I've got to get to Control," Rodney said. 

"I'll come with you." John couldn't let Rodney go unprotected. He grabbed Lorne's P-90 and called in a security team to the chair room. There would be no repeats of the last incursion. Sergeant Wu, the sergeant on deck, responded slowly with an affirmative, saying, "Tell the major we'll be there in two."

It was only after John had left with Rodney that he realized he had no authority at all; he'd called Wu out of pure habit, and Wu had still obeyed.

John hurried after Rodney down the corridor, into the transporter and down another hallway. Rodney stopped suddenly and then veered out to the East balcony; John followed him to stare at the sight of a Grodari fighter, stuck like a fly in amber within Atlantis' shield.

"Of course," Rodney said breathlessly. "That's how they do it."

"How they do what? What are they doing?"

"Can't you—? Of course you can't. I can see it. Remarkable. They're matching resonance—they must fly up slowly, so slowly, until they're barely touching, and then they can gradually match resonance with the shield. They must have delicate sensors, as delicate as my eye, to pinpoint the exact resonance. And my new algorithm changes, of course, but not frequently enough—that was the problem I couldn't pinpoint. Remarkable. I just have to get my laptop to the control room and send out an update to fix this."

"Well, let's go. C'mon," John said when Rodney didn't move fast enough.

"I never would have seen this," Rodney said as John dragged him down the hall. "My new eye made this possible."

"Well, good. I think it's pretty swell."

"You have no idea how much I—well, I've hated it, really. Was sickened by it. I was sure it would give me cancer or something. But right now I could kiss it."

"Pretty sure that's impossible. But I'll be happy to kiss it for you once this is all over, McKay."

Then they were in the control room. Rodney rushed to a console, plugged in his laptop, and started typing like a maestro. John approached Woolsey's office, hand on his radio. 

"Teyla. Ford. I'm in the control room. Cheesecake. Repeat, cheesecake."

_"Yes, sir. I'm at battle stations. Need a minute."_

_"I will be there, John."_

John leaned against a console and settled in to wait. _Atlantis, have you tried to communicate to the Grodari directly on their frequency?_

Atlantis sent an affirmative, explaining there was a lack, a space—no loci. Atlantis was not a unit. A unit was needed, or the communication was disregarded as noise. 

_Then it's like a princeps, only they have many princeps to make up their hive mind._

Affirmative.

Weird, but if true, it explained a lot. They needed to capture one of the units to explain to it; that unit could communicate to the hive mind.

If that were true—

Atlantis interrupted him with the wail of an impact siren. They'd been breached. 

"Chiú, Nervetti, Moran, with me," John said, only to hear Caldwell shout, "Sheppard! What the hell are you doing?"

"We have a breach on East D22, sir. I can lead them right to it."

Caldwell stared at him then said, "Very well. Go. We'll be right behind you."

John gave Rodney one last look. Rodney's face was stiff and determined, and he gave John a nod.

John took the marines and went. 

"We're going to try something different," John said to Lieutenant Chiú. "I have a device that might make it possible to communicate with the Grodari. If I can get even one of them to talk to me, it might be possible to end this thing. So we try to take them down without loss of life, but try to stun one of them long enough to disarm."

"Yes, sir." Chiú had been with the expedition since the beginning, which was why John had picked him, but John wasn't sure how far he wanted to test the guy's loyalty. He keyed his radio and got Teyla and Ford on their secure channel. "Guys, change of plans. We're heading to East D22."

He got two sets of clicks back, which must mean they had company.

 _"Sheppard. Shield changes are complete,"_ Rodney said in his ear.

"Acknowledged. Good job, Rodney."

The sound of plasma fire greeted John and his team when they piled out of the transporter, and John signaled the marines to stay back as he took point down the hallway to reconnoiter. The adrenaline was shooting through him; he'd never mention this to Carson, but the rush was even stronger with his new heart. Everything felt unnaturally crisp and clear.

There was a lot of visible damage in this section; the Grodari appeared intent on causing as much destruction as possible, but down here on 22 there weren't any crew, just unused labs and quarters. John gestured for the marines to join him, and then he sped to the opposite corner.

A Grodari saw him immediately, its gray face opening in a wide snarl, and it raised its cannon and fired. John ducked back into the shelter of the corner and waited for an interruption in the firing so he could try to use the translation device. But there was no let up of the blasts, and his cover was being eaten away. The noise and heat were tremendous. 

Atlantis sent him a frantic thought: the chance for peace would die with John. Please. They are a hive mind, and there is another much further away. Another chance. Finally, ducking low and throwing his hand around the edge, John fired his laser pistol in three long pulses. The Grodari roared and started stomping forward, and Chiú joined the fight, providing cover fire. John ducked his head out and fired again, this time hitting the implant on the Grodari's forehead. It collapsed to the deck.

He saw another Grodari come clomping over from much further down the corridor. He wasn't sure where the others were—maybe they'd gone in the other direction—but this was his chance. He pulled the transmitter from his vest.

Just then, Moran came out of cover and raised his pistol, eager to take the shot.

"No! Stand down, Moran!" John yelled.

Moran looked at him, then at Chiú. Chiú reached out and hauled him back. 

John didn't waste another second. He flipped on the transmitter and pointed it at the Grodari's head, his other hand on the wall. The Grodari was coming in fast—getting too close for comfort, really, its plasma cannon rising into firing position.

 _Atlantis, this had better work._ "Hold! Stop where you are!" John felt Atlantis do something wordless.

The Grodari took two more steps and then stopped.

_[This unit stops. Why?]_

Jesus Christ. It worked.

"This unit knows what you require. This unit wants to negotiate."

_[Negotiate? The whole requires unity. Your whole interferes with the perfection. You are the enemy of the perfection.]_ The Grodari raised its weapon. 

"No. We are not the enemy. We did not understand."

The Grodari tilted its head. _[The perfection is necessary for the unity. Your whole must not interfere.]_

"We do not want to interfere in the perfection." The perfection. The map of Grodari incursions flashed in his memory, and suddenly Atlantis/John understood. They needed all the geometric points of the dodecahedron for optimal communion of the hive mind. It was so simple.

Atlantis fed him the lines. "We did not understand the perfection. Now we understand. We want you to achieve the perfection."

_[You comprehend? The unity requires the perfection.]_

"Affirmative. To obtain the perfection, the whole must cease destruction. This unit can offer the whole the perfection without destruction."

The Grodari lowered its weapon. _[Destruction is not good. Destruction is wasteful.]_

"Affirmative. Destruction is wasteful. Cease destruction."

There was a long pause. _[Affirmative. Cease destruction. Your whole will help provide the perfection.]_

"Affirmative. In time. It will take time."

Pause. _[How much time?]_

John thought furiously. "We must achieve our unity to offer perfection. Some time. Unity is hard to achieve but very good."

 _[Unity is good.]_ Two more Grodari came walking down the corridor with no urgency. _[Keep these units for communication. We will discuss perfection again soon.]_

"Affirmative. Can we land on the fourth planet and be part of the perfection?"

There was another pause. _[Affirmative.]_

"Sheppard! What the hell is going on here!" 

John spun around to face Caldwell and a team of marines. To John's surprise, Woolsey had come too, wearing his suit and carrying a book as if he were going to tea. John looked around for Teyla and Ford but they were nowhere in sight. He saw Caldwell smirk and got a bad feeling.

John held up his hands. "Sir, I've just successfully negotiated a cease fire with the Grodari. They basically just want embassies on twelve worlds." He gestured at the three Grodari standing passively in the hallway. "These three are ambassadors for the entire race. They're a hive mind."

"What's this? Negotiations?" Woolsey tried to step forward but was elbowed back by Caldwell.

"Impossible," Caldwell said. "You're full of crap."

"I heard the whole thing, sir," Chiú said. "Or, one side of it, at least. Pilot Sheppard held up that device and spoke to the Grodari, and it just stood there while he had a peace talk with it. They're seeking something called 'the perfection.'"

"Or Sheppard has a freeze beam and he made it all up," Caldwell said, sounding furious. Woolsey stepped away from him, looking dismayed. 

"Sir, Atlantis would be happy to replay the entire conversation for you. Both sides." John signaled Atlantis.

_[This unit stops? Why?]_

_"This unit wants to negotiate."_

_[Negotiate? The whole requires unity. Your whole interferes with the perfection.]_

Caldwell swiped his hand, and John stopped the playback. 

"You could have manufactured that in your quarters." 

Chiú made a sound of protest.

John stepped forward. "The Grodari can be negotiated with. I'm wondering why, sir, when Atlantis rejected you as Pilot for withholding this very information, you would be so eager to discredit me for revealing it. What do you have against peace?"

"Commander Caldwell," Woolsey said, censure in his voice. "I'm afraid I will have to ask you to—"

That did it. Caldwell's eyes flashed gold, making Chiú and the other marines gasp. But Teyla and Ford weren't here, and John was kind of screwed, because Caldwell's next act was to swing out his palm, a device on it flashing and sending John flying. 

The charge struck him directly in the chest, but his heart, his new heart, wasn't fazed at all. It just kept right on beating. John laughed a little, then choked with dismay when his new friend, the Grodari, raised its plasma cannon and fired right at Caldwell.

"No," John gasped instinctively, because underneath the Goa'uld was a decent Star Force officer. But Caldwell had a shield that just absorbed the impact of the blast; he was completely unaffected.

That was when Woolsey smacked Caldwell hard on the head with his book, rendering him unconscious.

" _Regulatory Aspects of International Law_ ," Woolsey said in the resulting moment of stunned silence. "It's heavy reading."

John just nodded in relief.

:::

John's first act with his brevet command was to find out what the hell had happened to Teyla and Ford. Fortunately, it turned out the effects of Caldwell's stealthy stun blast were only temporary. They woke up groggy and pissed off in Carson's infirmary, seriously disappointed to learn they'd missed all the action.

"But you truly can communicate with them?" Teyla asked, and her voice was so exhausted and hopeful that John had to reach out and awkwardly pat her wrist.

"Atlantis can." Rodney said contentedly. "And as soon as we databurst the other City-ships, they'll be able to as well. We just need to send them my specs on the device and the translation matrix. Except, of course, we're going to hold a peace summit, so it's all pretty moot." 

Teyla stared at him with wide eyes. Ford made an angry sound. 

"What?" Rodney munched his nutrition bar.

"Two years," she said. "Two years of needless deaths."

"It's not Caldwell's fault," John said. "Or, at least, not the Caldwell you remember from the _Daedalus_. He was possessed by a Goa'uld sometime before he became Commander."

"I believe I will take a nap," Teyla said. "And then I would like a sandwich."

Ford grunted his agreement. "And you guys are fetching 'em." He rolled over and went back to sleep.

John's next action was to put himself right back in the chair so he could make the landing on P5Q-563. Not that they were in combat any longer, but there was a possibility the peace might not hold as they approached the planet, and he wasn't risking Atlantis to Lorne's skill with the drones, no matter how well the man had scored in simulation.

John shouldn't have worried, though. They passed peacefully through the cordon of Grodari ships. Rodney chattered away nervously by John's side the entire way down through the atmosphere, and then they touched down, light as a feather, only twenty-one feet off target.

"That's 6.4 meters, Commander," Rodney said. "I think your concentration slipped a little at the end, there."

"It did not. The portside flaps are bent out of true. Now that we're here, Atlantis can get fixed up right." 

Atlantis hummed a distinctly masculine smugness. John patted the arms of the chair and then eased upright. He had a meeting with Woolsey to debrief on the Caldwell situation. 

Poor Woolsey. He was vacillating between being seriously pissed off and in the next second telling John he should have realized a good-looking guy like Steven would never have been seriously interested in him. John just kept pouring the wine and patting him on the arm. As soon as Rodney had the gate synced, they'd be sending Caldwell back to SGCC along with a hell of a databurst. 

What happened afterward was anybody's guess. So far, things were looking up. Woolsey had a lot of confidence in him. But John had a summit to plan, and for that he'd need Teyla and Ford's knowledge, and Rodney's tech. Together, with Atlantis' help, John knew they could make peace happen in Pegasus. 

"Where are you going?"

"I have a meeting with Woolsey in half an hour."

"Oh, no you don't." Rodney grabbed his arm and hauled him toward the transporter. Once inside, he hit an unfamiliar quadrant. 

"You kidnapping me?"

"In a matter of speaking. More like pressing into service." He shoved John down the hallway, and John leaned back into his hands, happier than he could articulate that Rodney was alive and with him and being his usual, pushy, annoying self. "Jesus, you weigh a ton."

"Are you saying I'm fat?" John leaned back harder. "Because Mom always said I'm big boned."

"I'm saying you should lay off the Mallomars."

"Mmm. Mallomars. I wish."

"Yeah." Rodney yanked him to a halt, waved open a doorway and shoved him inside. 

"Wow." The quarters were incredible, on a corner with an amazing two-seventy view of Atlantis. "Is this your place?"

"No. It's yours," Rodney mumbled. "Well, it could be ours. It's big enough. I mean, should you be in need of a roommate."

John started laughing. 

"What? What?" A thunderous frown wrinkled Rodney's forehead.

"I'm just thinking: I'm glad I didn't invite you to move into my old place. Some jerk assigned me the crappiest quarters you've ever seen."

"Oh, ha-ha and ha." But Rodney was smiling hesitantly. 

"So." John leaned in and rested his forehead against Rodney's. "You bring the fondue pot, and I'll dig up my leather ottoman."

"You say the most romantic things. Seriously, I think my heart will stop, Sheppard."

"Shut up and kiss me."

"That's better." Rodney's mouth was the same, warm and flexible, his tongue pushy as it slipped beneath John's. Rodney's hands moved restlessly over John's back then moved to his front and started in on his tac vest. John helped, suddenly frantic to be rid of it, and they broke apart, grinning at each other as they both unzipped and shed their vests and gear. 

Rodney wrinkled his nose. "I think you smell like Grodari," he said as John shucked his T-shirt, and then Rodney seemed to be struck speechless.

Oh. John had clean forgotten. 

"What in God's name did you do—" Rodney stepped forward, hands outstretched, and brushed his fingertips over John's hairless chest.

John shivered. "There wasn't much point in keeping any of it." He paused and added, "Weird, huh?"

"I wouldn't say weird so much as...no, weird covers it." Rodney flattened his hand and ran his palm from John's collarbone down to his ribs.

This time, John full on shuddered. He hadn't realized how sensitive his skin was without the hair. Or maybe it was because Rodney was touching him again.

"Interesting," Rodney said. "I can see so much more, you know. I have incredible magnification with this thing." He gestured at his eye. And then he pinched John's nipple.

"F-fuck."

"Very nice," Rodney said, curling his lip. "Let's take this to bed."

"You've gotten over the weird, then," John said, and he wasn't just talking about his chest hair. 

"I have a very flexible mind." 

John couldn't argue with that, especially when they'd gotten naked and Rodney climbed on top of him and started running his tongue all over John's chest. 

"Jesus fuck, Rodney." John squirmed, trying to get more of his dick in contact with the warm skin of Rodney's belly. 

"Yes, fucking. We should try fucking. It's been too long."

"Oh, yeah." John smacked his hand down on Rodney's ass, the ass he'd been watching for weeks now, bouncing and flexing and making him just a little spacey.

"Wait a minute—who says you get first dibs?"

John craned his neck and gave Rodney a disbelieving look. "I just brokered a cease fire for the entire galaxy!"

"And hail conqueror, well met. That doesn't mean you get to plunder my ass."

"But, Rodney, you like being plundered." John gave his ass a squeeze.

"True. But it's the principle of the—"

"Please?"

"Oh, my God. You did not just flutter your eyelashes at me. Fine."

"Yes!" John rolled off the bed and then stopped with his hand on the built-in drawer. "Hang on. We've got nothing here."

"Idiot. Do you really think I dragged us here for connubial fun and games without preparing in advance? Check my pockets."

_Connubial?_

Atlantis sent him a series of images, all of which made John feel faint. He grabbed Rodney's pants and dug out a couple of condoms and a small tube of lube.

Rodney had turned onto his belly and propped his ass up. John took a long moment to take in the sight. "Oh, that's nice," he said appreciatively. 

"Thanks, hero. Now hurry it up. I only pushed back your meeting an hour or so."

But Rodney went quiet when John worked his fingers inside him; John had to lean over him and listen close to hear his little gasps of pleasure. This was always John's favorite part, when Rodney shut down the thinking machine and just started feeling. And John did his best to get him there, pushing in slowly, so damned slowly, until his thighs were trembling, and he looked down to where they were joined and saw Rodney pushing back, trying to get him deeper.

"Yeah, that's it, babe," John said. Rodney let out a huff of objection, but the back of his ears were pink. John leaned over him, covering him, pushing one knee up so he could get as close as possible, and started moving smoothly, in and out, rocking his hips. John fucked in and out and in again, and Rodney started moaning like a cat, the vibrations traveling through Rodney's body and into John's chest, where John's heart kept speeding faster. 

"Oh, God, yeah," John said, shoving a little harder, wanting Rodney to feel it. He curled his arm down and held Rodney's dick, gave him something to fuck into, and Rodney rode John's hand, pushing back onto John's cock, his plump ass smacking into John's groin.

"So sweet," John said. 

"Fucker," Rodney said.

"Yeah, I'm your fucker," John said, catching Rodney's earlobe with his teeth.

"John," Rodney groaned, and John squeezed his cock a little harder. That was all it took for Rodney to start coming, his ass clenching down on John's cock, his spunk covering John's hand. John fucked him gently through it, then pulled out when Rodney twitched with an unhappy sound. John leaned over and kissed Rodney's crazy eyebrow.

"Mmmm," Rodney said.

John stripped off the condom and tossed it, then considered jerking off on Rodney's ass for a finale, but Rodney rolled over and pinned him to the bed.

Grinning up at him, John said, "What is it, sweetheart?" 

"Don't even pretend you weren't going to jerk off on my ass."

"Who's pretending? I just thought I deserved a treat."

Rodney shook his head. "Not tonight, _sweetheart_. However, I think I can arrange a reward." He reached for the bottle of lube and slicked up a couple of fingers, tilting his misshapen eyebrow at John. "I know you love something up your ass when you come."

"You say that like it's a bad thing." It wasn't. It was awesome.

"No complaints here," Rodney said, bending over John's cock. Then—oh, hell yeah—Rodney's mouth was definitely his finest feature, especially when it was wrapped, smooth and warm, around John's cock, and his slick fingers were rubbing against the spot behind John's balls, then sliding back and in, fast and certain and right on target, his other fingers jammed against John's cheeks.

He fucked John fast with his fingers while his mouth moved lazily up and down, and John was already so close it wasn't fair—he couldn't take the time to really appreciate how goddamned good his boyfriend was at this. But the best thing of all was they'd be living together and they could do this all the time, every night, in fact, because the one thing John knew for sure was he was never losing Rodney again. Never. Rodney was the biggest part of the equation.

On that thought, John came his brains out.

When he came back online, Rodney was making gargling noises in the bathroom. 

Some things never changed.

:::

The princeps of Akrotiri, Helike, and Amaya arrived in grand fashion. 

As they stepped through the gate one by one, John, Woolsey, Teyla, and Ford bowed and waited for the next. First, Ronon Dex of Sateda arrived, then Mara Tanius of Lagos, and finally Ladon Radim of the Genii. 

"Welcome, princeps," Woolsey said. They all bowed in sync, and immediately turned to John, who said, "Atlantis welcomes you. It has much to tell you. This is a summit of peace, the first such summit between the humans of Pegasus and the Grodari. And so we must also give our welcome to the representatives of the Grodari."

He turned and lifted his transmitter, saying, "The City-ships of Pegasus wish to greet the unity."

John knew Atlantis, with Rodney's help, had prepped the other City-ships over data bursts, because when the Grodari stepped into the gate room and fanned out before them, all the princeps kept their cool, although John noticed Dex's fingers twitching near his holster. 

"Citizens of Pegasus—welcome to the Summit of Peace."

 

...............................  
September 6, 2014  
San Francisco, CA

  
[Comments also welcome on my LJ](http://esteefee.livejournal.com/181964.html).

**Author's Note:**

> Warnings:  
> Both John and Rodney are injured pretty severely pre-story and require biocybernetics (prostheses) as implants. The accident itself is explored—not too graphically, but those with triggers should be warned.
> 
> Also, there is an undercover Goa'uld on base with an implied sexual relationship with one of the other characters. This relationship is never explored. Since the Goa'uld is undercover, the relationship is in no way abusive, but the implication is still ugly.
> 
> For anyone curious, [This](http://www.iflscience.com/plants-and-animals/strange-reptile-fossil-discovered-china) is what the unacus looks like. Spelling changed to preserve the innocent fossil.
> 
> Source Image Credits:  
> http://www.escuelapedia.com/wp-content/uploads/Sistema-binario.jpg - 10101 binary file  
> http://i.ytimg.com/vi/NzX4xZL3Yys/maxresdefault.jpg - clockwork heart  
> http://en.wikipedia.org/wiki/Stargate_Atlantis - map of Atlantis  
> http://wonderfulengineering.com/hd-desktop-technology-wallpaper-backgrounds-for-download/ - tech textures  
> Tristan Bullard - tech wallpaper - code lines at bottom  
> All other images - screenshots from DVD/BluRay editions of Stargate Atlantis, credit MGM.
> 
> Image research assistant: mischief5.livejournal.com


End file.
